plotSpikeCI              package:CALIB              R Documentation

_p_l_o_t _s_p_i_k_e _c_o_n_c_e_n_t_r_a_t_i_o_n _v_s _m_e_a_s_u_r_e_d _i_n_t_e_n_s_i_t_y

_D_e_s_c_r_i_p_t_i_o_n:

     plot spike known concentration and measured intensity of one
     array.

_U_s_a_g_e:

     plotSpikeCI(spike, parameter,array = 1, bc = FALSE, area = TRUE, 
                 meanpoint = TRUE,xlab = "log(Concentration)",
                 ylab = "log(Intensity)", main = colnames(spike$R)[array],
                 onlycalib = TRUE, xlim = NULL, ylim = NULL, pch = 19,
                 cex = 0.2, meanpch = 21, meancex = 1, lwd = 1.5, 
                 cy5col = "red", cy3col = "green", ...)

_A_r_g_u_m_e_n_t_s:

   spike: a 'SpikeList' object.

parameter: a 'ParameterList' object.

   array: integer giving the array to be plotted. 

      bc: a logical value. 'TRUE' means background corrected measured 
          intensities are used. Default is FALSE.

    area: a logical value. 'TRUE' means spot area is used to calculate 
          measured intensities. Namly, measured intensities are
          calculated by  foreground intensities(or background corrected
          intensities, if bc is  'TRUE') multiply spot area. 'FALSE'
          means spot area is not used. Default is 'TRUE'.

meanpoint: a logical value. 'TRUE' is to show meanpoint of measured
          intensities with the same concentration on the plot. 'FALSE'
          means not show. 

    xlab: a title for the x axis.

    ylab: a title for the y axis.

    main: an overall title for the plot.

onlycalib: a logical value. 'TRUE' means only the calibration controls
          are on  the plot. 'FALSE' means to plot all the spikes

    xlim: the x limits (min,max) of the plot.

    ylim: the y limits of the plot.

     pch: a integer code for one of plotting characters or symbols for
          the spike data set. Default is 21.

     cex: a numerical value giving the amount by which the points which
          indicate spike data set should be scaled relative to the
          default. Default is 0.4.

 meanpch: a integer code for one of plotting characters or symbols for
          the meanpoints. Default is 21.

 meancex: a numerical value giving the amount by which the meanpoints
          should be scaled relative to the default value. Default is 1.

     lwd: width of the model curves. Default is 1.5.

  cy5col: color of all symbols for cy5. Default is red.

  cy3col: color of all symbols for cy3. Default is green.

     ...: other graphical parameters can be used in function 'plot'.

_D_e_t_a_i_l_s:

     The function plots spike concentration and measured intensity of
     one array.  array number is specified by the argument 'array'. It
     accepts the concentration of given array from the agrument
     'spike', which is a 'SpikeList' object. The measured intensities
     are calculated from 'spike'. Four different ways can be used to
     calculate the measured intensities. Arguments 'bc' and 'area' are 
     logical and their combinations are used for specifying the four
     differents ways.  'bc' indicates using background correction or
     not. 'area' indicates multipling  spot area or not. The default
     value of these two arguments are 'bc' = FALSE and  'area' = TRUE. 

     In order to help data visualization, meanpoints and model curve
     can be added on the plot. And the arguments 'meanpoint' and
     'parameter' are correspond to these. The meadians of every group
     of measured intensities which have the same concentration  are
     shown on the polt if 'meanpoint' is true. Model curves of both dye
     are  shown if the arguement 'parameter' is specified after
     parameter estimation.

_V_a_l_u_e:

     A plot is created on the current graphics device.

_A_u_t_h_o_r(_s):

     Hui Zhao

_S_e_e _A_l_s_o:

     see graphic functions 'plot', 'par'

_E_x_a_m_p_l_e_s:

     # load data: spike
     data(spike)

     # specify the array to be plotted.
     array <- 1

     # use the default values for other parameters.
     plotSpikeCI(spike,array=array)

     # after parameter estimation, the model curves can be shown on the plot.
     data(parameter)
     plotSpikeCI(spike,parameter,array=array)

